tbuckley/cabot-search huggingface dataset:
Abstract 73: A ubiquitination cascade regulating the integrated stress response and survival in carcinomas
Authors: Lisa D. Cervia, Tsukasa Shibue, Benjamin Gaeta, Ashir A. Borah, Lisa Leung, Naomi Li, Nancy Dumont, Alfredo Gonzalez, Nolan Bick, Mariya Kazachkova, Joshua M. Dempster, John M. Krill-Burger, Federica Piccioni, Namrata D. Udeshi, Meagan E. Olive, Steven A. Carr, David E. Root, James M. McFarland, Francisca Vazquez, William C. Hahn
Journal: Cancer Research (2022)

Abstract Targeting of mutated oncogenes has led to the identification of new targeted therapies. However, druggable oncogenes do not occur in most cancers. Systematic identification of signaling pathways required for the fitness of cancer cells will facilitate the development of new cancer therapies. We used gene essentiality measurements in 793 cancer cell lines to identify selective co-essentiality modules and found that a ubiquitination ligase complex composed of UBA6, BIRC6, KCMF1 and UBR4, which encode an E1, E2 and two heterodimeric E3 subunits, respectively, is required for the survival of a subset of epithelial tumors. Suppressing BIRC6 in cell lines that are dependent on this complex led to a substantial reduction in cell fitness in vitro and potent tumor regression in vivo. Mechanistically, BIRC6 suppression resulted in selective activation of the integrated stress response (ISR) by stabilization and upregulation of the heme-regulated inhibitor (HRI), a direct ubiquitination target of the UBA6/BIRC6/KCMF1/UBR4 complex. These observations uncover a novel ubiquitination cascade that regulates ISR and highlight the potential of ISR activation as a new therapeutic strategy. Citation Format: Lisa D. Cervia, Tsukasa Shibue, Benjamin Gaeta, Ashir A. Borah, Lisa Leung, Naomi Li, Nancy Dumont, Alfredo Gonzalez, Nolan Bick, Mariya Kazachkova, Joshua M. Dempster, John M. Krill-Burger, Federica Piccioni, Namrata D. Udeshi, Meagan E. Olive, Steven A. Carr, David E. Root, James M. McFarland, Francisca Vazquez, William C. Hahn. A ubiquitination cascade regulating the integrated stress response and survival in carcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 73.
Abstract 6390: Chromosome arm aneuploidies as genetic vulnerabilities of triple-negative breast cancer
Authors: Rohan Dandage, Michael Schwartz, Lynn Karam, Traver Hart, Elena Kuzmin
Journal: Cancer Research (2022)

Abstract Triple-negative breast cancer (TNBC) is a subtype of breast cancer which lacks the expression of key biomarkers, namely Estrogen and Progesterone receptors and HER2. Therefore, it lacks targeted therapies, resulting in the worst prognosis compared to other breast cancer subtypes. Chromosome 4p (chr4p) loss is recurrent in TNBC, correlates with poor prognosis, is an early event in tumor evolution, and confers a proliferative advantage onto cells. Here, we propose that chr4p loss can be leveraged as a genetic vulnerability of TNBC by identifying its specific synthetic lethal (SL) genetic interactions. An SL interaction occurs when the inactivation of individual genes is tolerated, however, the combined inactivation of the corresponding genes leads to a loss of cellular viability. SL interactions offer promising avenues for precision oncology therapeutic strategies of TNBC. We leveraged the publicly available CRISPR-mediated genome-wide gene inactivation screens (DepMap project) dataset to computationally predict pairwise SL interactions that are specific to individual genes within chr4p, as well as complex SL genetic interactions involving multiple genes spanning large segments of chr4p and the entire chromosome arm. We developed regression models to compare the inactivation effect of a given SL partner gene, between cell lines that harbor chr4p loss and those characterized by a copy-neutral status of chr4p, while effectively accounting for potential confounding effects. We integrated the putative SL interactions identified from these regression models with those identified using other methods, drugZ and MAGECK, therefore, resulting in a robust set of putative SL interactions. We have prioritized the SL interactions for their subsequent experimental validation in TNBC PDX-derived 2D and 3D cell models, which we will carry out using CRISPR-based gene editing. The prediction model and collective set of SL candidates identified in this study is a unique resource for the development of SL-based therapeutic strategies for TNBC and other cancers harboring chr4p loss. Citation Format: Rohan Dandage, Michael Schwartz, Lynn Karam, Traver Hart, Elena Kuzmin. Chromosome arm aneuploidies as genetic vulnerabilities of triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6390.
Abstract 2278: Expanding cancer therapy options by leveraging synthetic lethal interactions between druggable paralogs
Authors: Phoebe C. Parrish, James D. Thomas, Austin M. Gabel, Shriya Kamlapurkar, Robert K. Bradley, Alice H. Berger
Journal: Cancer Research (2022)

Abstract Synthetic lethal therapies are a promising approach to expand therapeutic options for cancer patients. Since synthetic lethal therapies target tumor cells specifically, they have fewer off-target effects than oncogene targeted approaches. To identify new cancer drug targets, we focused on paralogs, ancestrally-duplicated genes that frequently retain redundant or overlapping functions. To find synthetic lethal human paralogs, we developed paired guide RNAs for Paralog gENetic interaction mapping (pgPEN), a pooled CRISPR-Cas9 single and double knockout approach targeting over 2,000 paralogs. We applied pgPEN to two cancer cell lines and found that 12% of human paralogs exhibit synthetic lethality in at least one context. To our knowledge, pgPEN represents the largest experimental assessment of human paralog synthetic lethality to date. We next identified paralog pairs to prioritize for follow-up study. A key drawback to synthetic lethal therapies is that many genetic interactions are context-dependent. To identify likely penetrant interactions, we compared our data to other published paralog screens and computational predictions of paralog synthetic lethality. We found that over 75% (n=96) of pgPEN hits were predicted to be broadly synthetic lethal, and nearly 10% (n=10) of pairs were synthetic lethal in multiple paralog screens. Finally, we prioritized paralogs targeted by existing small molecule therapies. Of the 122 synthetic lethal pairs identified by pgPEN, 16% (n=20) are currently druggable. We mined drug repurposing data from DepMap to find pairs where a paralog-targeting drug showed a stronger effect in cell lines with low target gene copy number or expression relative to cell lines with normal target gene copy number or expression. These drugs could selectively target cancer cells in cases where one or both paralogs is lost in tumors but retained in normal tissue. We also leveraged The Cancer Genome Atlas tumor sequencing data to find paralog pairs where one member is recurrently lost in cancer. Taken together, these studies identify druggable, highly penetrant synthetic lethal paralog interactions. In combination with tumor sequencing data, we identify high-priority paralog drug targets that can be further tested and translated to the clinic. Paralog synthetic lethal therapies could provide a relatively low-toxicity therapeutic approach to improve the efficacy of cancer treatments and prevent the emergence of acquired resistance. Citation Format: Phoebe C. Parrish, James D. Thomas, Austin M. Gabel, Shriya Kamlapurkar, Robert K. Bradley, Alice H. Berger. Expanding cancer therapy options by leveraging synthetic lethal interactions between druggable paralogs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2278.
Abstract 1912: A versatile computational pipeline for the preprocessing of cell-free DNA fragmentation data
Authors: Ivna Ivankovic, Zsolt Balázs, Todor Gitchev, Daniel Trejo Banos, Norbert Moldovan, Panagiotis Balermpas, Jonas Willmann, Nicolaus Andratschke, Florent Moulière, Michael Krauthammer
Journal: Cancer Research (2022)

Abstract Cell-free DNA (cfDNA) emerges as a promising liquid biopsy biomarker for cancer diagnosis and patient monitoring. Complementing mutation-based assays, cfDNA carries information about epigenetic modifications from decaying cells. This information is encoded in the shape of the cfDNA fragments. Specifically, fragments from cancer tend to be shorter than those originating from other adult cells, enabling a distinction between cancer patients and healthy individuals. Additional cfDNA features such as fragment end motifs and information on nucleosome positioning provide further insight into cancer biology. These cfDNA measures are typically inferred from low-pass whole genome sequencing and subsequent bioinformatics processing. A key bioinformatics step is the alignment of DNA sequencing reads to the reference genome, which critically depends on preprocessing steps such as read trimming and alignment filters. A good understanding of preprocessing settings is thus crucial to derive accurate information from cfDNA. We therefore investigated to what extent preprocessing choices affect cfDNA analysis. To this end, we have built a robust bioinformatics pipeline that evaluates a range of possible preprocessing settings. The pipeline is implemented in a bioinformatics workflow engine, enabling a scalable and reproducible workflow. We are currently evaluating the effect of preprocessing on global and regional fragmentation patterns, detection of nucleosome positioning and identification of fragment end motifs. The different preprocessing settings are also evaluated for their ability to distinguish cancer from control samples using cfDNA fragmentation information. We are benchmarking the pipeline using cfDNA datasets from multiple centres to ensure our findings are generalizable over different platforms and experimental procedures. Our investigations will allow us to build a versatile bioinformatics preprocessing pipeline for the analysis of cell-free DNA fragmentation data. Citation Format: Ivna Ivankovic, Zsolt Balázs, Todor Gitchev, Daniel Trejo Banos, Norbert Moldovan, Panagiotis Balermpas, Jonas Willmann, Nicolaus Andratschke, Florent Moulière, Michael Krauthammer. A versatile computational pipeline for the preprocessing of cell-free DNA fragmentation data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1912.
Abstract 3993: ERO1α as a potential target in EGFR driven non-small cell lung cancer
Authors: Brennan D. Johnson, Wei-Chih Chen, Werner J. Geldenhuys, Lori A. Hazlehurst
Journal: Cancer Research (2022)

Abstract Endoplasmic Reticulum Oxidoreductase-1 alpha (ERO1α) is an endoplasmic reticulum (ER) resident protein responsible for oxidation of Protein Disulfide Isomerase (PDI). The molecular interactions between ERO1α and PDI allow for proper protein folding to occur. Recent reports indicate that ERO1α expression is a poor prognostic indicator of survival in multiple cancer types including multiple myeloma, lung cancer, esophageal carcinoma, hepatocellular carcinoma, and diffuse large B-cell lymphoma. In this study we utilized genetic strategies to determine the role of ERO1α in EGFR driven Non-Small Cell Lung Cancer (NSCLC). Our data indicate that CRISPR knockout of ERO1α leads to decreased clonogenicity in both PC-9 and HCC4006 cell lines. The phenotype can be partially rescued upon addition of conditioned media derived from the control cell lines. The data suggest that ERO1α expression is required for correct protein folding of a secreted factor that contributes to clonogenicity and growth. PC-9 ERO1α knockout cells injected into SCID-Beige animals led to increased overall survival (OS) compared to animals injected with PC-9 control cells. (PC-9 Control OS = 100 days, PC-9 ERO1α Knockout OS =154 days p=0.0045 **). Interestingly, ERO1α knockout cell lines still maintained sensitivity to standard of care agent Osimertinib. We identified T151742 as an ERO1α inhibitor that was approximately 2-fold more potent compared to the previously published ERO1α inhibitor EN460. A cellular thermal shift assay was performed to determine specificity of T151742 toward ERO1α compared to other FAD containing enzymes. We show that T151742 had a higher specificity towards ERO1α in comparison to other flavoenzymes such as ERO1β and LSD-1. Finally, our data indicate that PC-9 ERO1α knockout cell lines were ~2-fold resistant to T151742 by MTT but were completely resistant when using a 3D cell culture model suggesting T151742 is reliant on ERO1α in a 3D system. Finally, treatment of PC9 and HCC4006 cells with T151742 in combination with Osimertinib was synergistic in vitro. Taken together, this suggests ERO1α may be a viable target for EGFR driven NSCLC and that future studies will elucidate the use of T157142 in vivo as a single agent and in combination with EGFR inhibitors using in vivo studies. Citation Format: Brennan D. Johnson, Wei-Chih Chen, Werner J. Geldenhuys, Lori A. Hazlehurst. ERO1α as a potential target in EGFR driven non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3993.
Clinical evaluation of the BioFire Global Fever Panel for the identification of malaria, leptospirosis, chikungunya, and dengue from whole blood: a prospective, multicentre, cross-sectional diagnostic accuracy study
Authors: Yukari C Manabe, Joshua Betz, Olivia Jackson, Victor Asoala, Isabel Bazan, Paul W Blair, Aileen Chang, Sarunyou Chusri, John A Crump, Kimberly A Edgel, Dennis J Faix, Stefan Fernandez, Anne T Fox, Jose A Garcia, Max Grogl, Erin A Hansen, Vireak Heang, Stacey L House, Krisada Jongsakul, Michael B Kaburise, Chonticha Klungthong, Mohammed Lamorde, Andrew G Letizia, Ivette Lorenzana, Malen Luy, Vanance P Maro, Christopher N Mores, Christopher A Myers, Abraham R Oduro, Leda Parham, Abigail J Porzucek, Michael Prouty, David S Rabiger, Matthew P Rubach, Crystyan Siles, Maria Silva, Chinaka Ukachu, John N Waitumbi, Cynthia L Phillips, Brian W Jones
Journal: The Lancet Infectious Diseases (2022)
Myocardial Fibrosis Assessment Using T1 and ECV Mapping With Histologic Validation in Chronic Dilated Cardiomyopathy
Authors: Anne G. Raafs, Bouke P. Adriaans, Michiel T.H.M. Henkens, Job A.J. Verdonschot, Mitch J.F.G. Ramaekers, Suzanne Gommers, Myrurgia A. Abdul Hamid, Simon Schalla, Christian Knackstedt, Vanessa.P.M. van Empel, Hans-Peter Brunner-la Rocca, J.E. Wildberger, Sebastiaan C.A.M. Bekkers, Mark R. Hazebroek
Journal: JACC. Cardiovascular imaging (2022)
Abstract 5080: Age- and pregnancy-related impact on soluble immune checkpoint protein profiles in mice as analyzed by a novel multiplex immunoassay
Authors: Wen-Rong Lie, Christine Kornmeier, Ling Zeng, James Hoberg
Journal: Cancer Research (2022)

Abstract Immune checkpoint proteins are key regulators of the immune system and drug targets of cancer immunotherapy. There is extensive literature on the use of various types of mouse models for biomarker discovery and drug testing. Only a few studies have examined the association between soluble immune checkpoint proteins and the immune status. Following the development of multiplex immunoassay panels for profiling human co-inhibitory and co-stimulatory immune checkpoint proteins, here we report the development of a novel magnetic bead-based Luminex multiplex assay for the quantitative detection of 28 mouse immune checkpoint proteins and immune regulators in 25 μL of sample (PD-1, PD-L1, PD-L2, CTLA-4/CD152, TIM-3, LAG-3, B7-H2/ICOSL, B7-H3/CD276, BTLA, GITR, HVEM, CD27, CD40, CD80/B7-1, CD226/DNAM-1, 4-1BBL/TNFSF9, CD137/4-1BB, 5’-NT/CD73, BCA-1/CXCL13, CD25/IL-2Rα, Granzyme B, E-cadherin, Galectin-1, Galectin-3, IFNγ, IL-10, TLR-2, and TNFα). Immune function declines with age, while the incidence of cancer rises. In this study, we examined age-related serum samples by quantitative profiling soluble checkpoint proteins from young (age of 8-month-old, n=8) and old-aged mice (48-month-old, n=8) of C57BL/6 strain. A significant age effect was observed on the levels of soluble checkpoint proteins in mouse serum samples tested. Comparing with the young mice, decreased levels of circulating HVEM, Granzyme B, LAG-3, PD-L1, CD73, B7-H2, CD25, and CD27; and increased levels of circulating TIM-3, PD-1, PD-L2, CD40, Galectin-3, IL-10, BCA-1, and TLR-2 were observed in aged C57BL/6 mice (Mann Whitney test, P value &amp;lt;0.05). The immune system also changes during pregnancy. We used the similar multiplex array approach to profile the soluble checkpoint proteins in non-pregnant (n=16) and pregnant CD-1 mice (n=9). Significant decreased levels of soluble LAG-3, B7-H2, B7-H3, CD25, CD27, and Galectin-1; and significant increase of soluble CD137, Galectin-3, and CD73 expression levels were detected in the serum samples of pregnant mice, as compared to the samples from the non-pregnant mice (Mann Whitney test, P value &amp;lt;0.05). Altogether, using bead-based quantitative multiplex analysis, our results demonstrate that the changes on circulating immune checkpoint protein profiles occur in the immunologic adaptations with age and during pregnancy in mice. Citation Format: Wen-Rong Lie, Christine Kornmeier, Ling Zeng, James Hoberg. Age- and pregnancy-related impact on soluble immune checkpoint protein profiles in mice as analyzed by a novel multiplex immunoassay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5080.
Abstract 3392: Rapid, scalable isolation of human tumor nuclei for single cell genomics
Authors: Michael Gibbons, Alaina Puleo, Jill Herschleb, Sarah Taylor
Journal: Cancer Research (2022)

Abstract Sample preparation remains a significant roadblock to the implementation and scaling of single cell technologies in clinical and translational research. Time consuming, custom dissociation protocols performed on fresh tissue by experts are often utilized to obtain high quality single cell data. However, these complex protocols result in low sample throughput and high variability driven by logistical challenges and user variability. Additionally, many samples that are of interest for clinical and translational studies arrive in research labs snap frozen, leaving nuclei extraction as the only viable path to generate single cell/nuclei data. To overcome these challenges, we present a scalable, easy to use, spin column-based nuclei isolation platform that generates single nuclei that are ready for input into downstream 10x Genomics single cell assays in under an hour. We processed eight unique human tumors in parallel (skin melanoma, breast, ovary, prostate, lung, kidney, colorectal, and pancreas). Starting from snap frozen tissue, we were able to generate single nuclei suspensions for all samples, in parallel, within 90 minutes. The resulting single nuclei were run through the 10x Genomics Single Cell Gene Expression, Single Cell Immune Profiling, and Single Cell ATAC workflows. Single cell gene expression data retained high data complexity across all tumor types tested. Expected cell type clusters, including tissue-specific tumor cells, surrounding/infiltrating immune cells and stromal cells were easily identified and profiled via gene expression analysis. Even fragile cell types often missing in single-cell data (e.g. mature adipocytes) were preserved and profiled in this experiment. Additionally, epigenetic changes as measured by Single Cell ATAC profiling were consistent with both general and tissue-specific epigenetics of each cancer type analyzed. In summary, this platform streamlines sample preparation for single cell studies from snap frozen tissue, enabling these samples to be used much more routinely and unlock biobanked sample cohorts. The findings presented here demonstrate that this fast and easy to use nuclei isolation system provides a consistent platform for generating high quality single nuclei data at scale for clinical, translational and basic research studies alike. Citation Format: Michael Gibbons, Alaina Puleo, Jill Herschleb, Sarah Taylor. Rapid, scalable isolation of human tumor nuclei for single cell genomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3392.
Abstract 2563: FAK inhibitor APG-2449 and CDK4/6 inhibitor palbociclib synergistically suppress mesothelioma tumor growth via autophagy induction
Authors: Ran Tao, Douglas D. Fang, Yuanbao Li, Guoqin Zhai, Feng Zhou, Qixin Wang, Jing Deng, Dajun Yang, Yifan Zhai
Journal: Cancer Research (2022)

Abstract Malignant mesothelioma is a rare but highly lethal malignancy, with a 5-year survival rate of less than 10%. Current treatment, which combines surgery, chemotherapy, radiation, and immunotherapy, yields marginal benefit and ultimately results in drug resistance or recurrence. Therefore, developing more effective treatments is an urgent unmet need. Among the most common genomic abnormalities in mesothelioma are alterations of cyclin-dependent kinase inhibitor 2A/B (CDKN2A/B) and neurofibromin 2 (NF2). Combined CDKN2A deletions and NF2 loss is a negative prognostic factor for both progression-free and overall survival. Mesothelioma cells lacking expression of CDKN2A/B or NF2 are reported to be sensitive to CDK4/6 or focal adhesion kinase (FAK) inhibition, respectively. This study explored the potential utility of combining CDK4/6 inhibitor palbociclib and APG-2449, an investigational, clinical-stage ALK/ROS1/FAK inhibitor, in preclinical models of mesothelioma. Compared to controls and either single agent, the combination of palbociclib and APG-2449 enhanced inhibition of growth of cultured mesothelioma cells. This binary combination also synergistically induced durable antitumor activity in multiple murine mesothelioma models, including both cell line- and patient-derived xenografts. Mechanistically, treatment of mesothelioma cells with this combination likely downregulated FAK phosphorylation and enhanced cellular senescence and autophagy, as evidenced by an increase in the percentage of β-galactosidase-positive cells and upregulation in protein expression levels of autophagy markers P62 and LC3B. The combination also downregulated DNA damage-relevant proteins high mobility group box protein 1 (HMGB1) and γ-H2A histone family member X (ϒ-H2AX). Taken together, the data implicate that an interplay between autophagy and DNA damage repair contributes to the synergistic antitumor effects. In summary, our results unveil a novel potential therapeutic strategy of targeting both FAK and CDK4/6 in order to synergistically inhibit tumor growth in mesothelioma. The synergistic effects are evidently mediated by induced autophagy and enhanced cellular senescence. This preclinical study lays a foundation for future clinical development of APG-2449 combined with CDK4/6 inhibitors for mesothelioma. Citation Format: Ran Tao, Douglas D. Fang, Yuanbao Li, Guoqin Zhai, Feng Zhou, Qixin Wang, Jing Deng, Dajun Yang, Yifan Zhai. FAK inhibitor APG-2449 and CDK4/6 inhibitor palbociclib synergistically suppress mesothelioma tumor growth via autophagy induction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2563.